DNAMAN使用手冊(An Integrated System for Sequence Analy

1、 Sequence ManipulationSequence inputInformation exchangeEditingSequence composition and conversionBLAST documentsSequence inputDNAMAN provides 20 sequence channels to keep active sequences in memory. These sequence channels simplifymultiple functional analyses and substantially increase the efficien

2、cy of your works. A panel window shows the current working sequence. You may edit the sequence directly in the panel.Information exchangeDNAMAN accepts sequence files in GenBank, GCG, CUSTAL, FASTA, PIR and GDE format. It can export multiple sequences in GCG, CUSTAL, PIR and GDE format.DNAMAN provid

3、es a word processor for sequence editing. With this word processor, you can incorporate charts, images, graphics from any other Windows software into your documents.DNAMAN works as an object linking and embedding (OLE) server to exchange the information of restriction maps with other software. With

4、OLE, you can incorporate your restriction maps into other Windows applications, and directly modify the maps within the applicationsEditingEditing a text file with DNAMAN is as easy as working with your favorite word processor. With the word processor of DNAMAN, you can edit original sequence files,

5、 and the analysis results as well.Sequence composition and conversionDNAMAN reports the composition and molecular weight of a sequence.It performs the conversion of a sequence to its reverse, complementary, reverse complementary, double strand, and RNA sequencesBLAST documentsIn addition to accessin

6、g the Internet through Web browser, DNAMAN prepares a file in BLAST document formats with a query sequence for directly accessing BLAST E-mail Server. Five BLAST document formats are currently available: Blastn, Blastx, Tblastx, Blastp and Tblastn.Examples:Internet/Intranet BrowserDNAMAN provides an

7、 integrated Web browser to access to the Internet or your Intranet.You may load sequence from the brwoser for direct analysis.You may also work with the servers on the Internet.Sequence SearchSearch for nucleotide sequencesSearch for consensus sequencesSearch for open reading framesSearch for repeat

8、 sequencesSearch for amino acid sequencesSearch for nucleotide sequencesWith DNAMAN, you can search for nucleotide sequences from one or both strands of a DNA sequence. Gaps and ambiguous nucleotides are allowed in the query sequences. You may search for a list of query sequences on the target seque

9、nce.DNAMAN instantly reports the searching results in graphics. Colors and arrowheads indicate different sequence groups and sites. You may magnify any region of the DNA fragment and display the regional sequence of by selection.Search for consensus sequencesWith DNAMAN, you can search for DNA or pr

10、otein consensus sequences from both strands or six reading frames of DNA sequences. DNAMAN provides a database of DNA and protein consensus sequences. The database is expandable and editable. You can create custom consensus sequence databases.Search for open reading framesYou may search for open rea

11、ding frames from six reading frames of a DNA sequence. The searching results are shown in a text table. DNAMAN also provides a graphical view of the location of Start/Stop codons on a DNA sequence.Search for repeat sequencesYou may search for direct repeat and reverse repeat sequences from both stan

12、ds of a DNA sequence. You can also search for reverse complementary repeat sequences that may form hairpin/stem-loop structures.Search for amino acid sequencesYou may search for an amino acid sequence and its variations from the six reading frames of a DNA sequence. DNAMAN allows ambiguous amino aci

13、ds as well as a number of mismatches in a query sequenceRestriction AnalysisRestriction site analysisRestriction mapRestriction pattern illustrationElectronic cloningConstructing restriction mapsSilent mutationDirected mismatchRestriction site analysisYou can search any restriction site on a DNA seq

14、uence. DNAMAN supplies two restriction enzyme files; the restrict.enz file with 180 most frequently used restriction enzymes, and the dnamanre.enz file with 1364 enzyme records. You can also create your own enzyme files. All the enzyme files are editable and expandable.DNAMAN provides custom restric

15、tion enzyme filters on cutter, ends, frequency and methylation sensitivity. Users can define the DNA molecule as a linear or a circular type.DNAMAN reports the restriction analysis results in an easy-to-read table. The cutting sites are shown in alphabetical order of enzymes, and in site position or

16、der as well. The non-cutting enzymes are also listed. In addition, DNAMAN displays enzyme sites on the top of the DNA sequence.Restriction mapDNAMAN provides easy-to-use tools to produce publication-quality restriction maps. These tools can be used to draw linear or circular restriction maps with or

17、 without DNA sequence information. You can also draw maps for other projects, such as PCR strategy diagrams, gene structural maps, etc.DNAMAN accompanies with a high quality drawing program, LBDraw. Working with LBDraw, you can easily make sophisticated diagrams with many restriction maps.Restrictio

18、n pattern illustrationDNAMAN predicts the patterns of restriction enzyme digested DNA fragments in a gel electrophoresis. You can perform single enzyme digestion on multiple sequences, and single or multiple digestion on a single sequence. DNAMAN shows the information of restriction fragments on the

19、ir sizes and ends when you click on these fragments.Electronic cloningDNA cloning is a time consuming and expensive process. DNAMAN provides easy-to-use tools to design a cloning strategy and performs evaluation analyses on target sequences. This feature could improve the efficiency of your cloning

20、work in laboratory.DNAMAN mimics basic steps of the actual cloning process: Restriction analysis on the original vector and insert sequences Selection of vector and insert fragments from restriction pattern Verification of the end compatibility of DNA fragments Modification of fragment ends if neces

21、sary Insertion of linkers if necessary Producing the final clone sequenceConstructing restriction mapsDNAMAN can help you reconstruct a restriction map in the absence of DNA sequence. You must provide all fragment sizes in single and double digestion. DNAMAN deduces the possible restriction map(s) f

22、rom the information of restriction fragments.Silent mutation analysisSilent mutation analysis allows you to design a desired mutation site on a DNA sequence. This mutation will result in the modification of restriction property without changing the coding amino acid sequence. This function searches

23、for potential mutation positions to create or destroy restriction enzyme sites.Directed mismatch analysisDirected mismatch analysis allows you to create or remove restriction sites on a DNA sequence or its mutants (variants) by incorporating a single or double mismatch at a site near the mutation. U

24、sing this function you can create or destroy a restriction site in order to distinguish the wild type allele and a common mutant allele.Sequence AssemblySequence assembly methodSequence assembly editorSequence assembly methodDNAMAN uses fast alignment algorithms to assemble quickly and accurately a

25、large number of overlapping sequences. DNAMAN can automatically adjust the orientation of each fragment and remove vector sequences as well. You can set sensitivity parameters to control gaps and ambiguous sequences in contigs.Sequence assembly editorDNAMAN displays sequence assembly project in thre

26、e windows: Graphic window provides an overview of the assembly construction. You can edit this graphical presentation to produce high quality diagrams for publications.Name list window contains all assembled sequence names. You can change the sequence order by moving the sequence names in this windo

27、w.Sequence window shows all original sequences and a consensus sequence. You can edit any of the original sequences to improve the result of sequence assembly.DNAMAN exports sequence the assembly result in a text window. You have options of reporting the consensus sequence only, or all sequences inc

28、luding the consensus sequence and original sequences.Sequence Homology AnalysesDot matrix plotTwo sequence alignmentDot matrix plotWith DNAMAN, you may compare two DNA sequences or two protein sequences in a dot matrix plot. A specific algorithm is developed to yield high quality dot matrix plot. Wi

29、th this method, long DNA sequences can be compared in short time with little background noise. You may efficiently compare genomic sequence with the dot-matrix plot function of DNAMAN.DNAMAN displays the actual sequences and their alignment on any selected region in a sequence window.Two sequence al

30、ignmentDNAMAN uses fast or optimal algorithms to align two DNA or protein sequences. You have options to control the sensitivity of alignment. DNAMAN also allows you to select any region of target sequences for alignment.For DNA sequence alignment, you have an option to use the minus strand for comp

31、arison. For protein sequence alignment, DNAMAN can report the amino acid similarity of two protein sequences in a text window. The amino acid similarity matrix is editable by users.Multiple Sequence AlignmentMultiple sequence alignment methodsMultiple sequence alignment editorMultiple sequence input

32、 and outputPhylogenetic treesRestriction analysisHydrophobic / hydrophilic profileSecondary structure predictionMultiple sequence alignment methodsAlgorithmsDNAMAN uses ClustalW algorithm (Feng-Doolittle and Thompson) for Optimal Alignment, and the global alignment algorithm (Wilbur and Lipman) for

33、fast alignment. The three types of Optimal Alignment in DNAMAN provide high quality alignment results. With the Fast Alignment method, you may quickly align a large number of DNA or protein sequences. Parameters and MethodsYou may set different parameters to make adequate alignment for your DNA or p

34、rotein sequences. The multiple alignment function of DNAMAN is threaded. You may run up to 16 sets of multiple alignment simultaneously. You may also perform other sequence analysis while doing the multiple alignment.Multiple sequence alignment editorDNAMAN provides a high performance alignment edit

35、or. A graphical view of the alignment allows you to quickly move to an interesting region. You can change the alignment list order by drag and drop sequence names. You are also able to add or delete gap insertions, move a fragment within a gap and truncate aligned sequencesYou can modify the appeara

36、nce of multiple alignment sequences:displaying identical residues in colors or blocksdisplaying consensus sequencechanging text fontMultiple alignment input and outputYou can directly input sequences or multiple alignment profiles for alignment from the following sources: GenBank, EMBL/Swiss Prot, G

37、CG/MSF, CLUSTAL, FASTA, NBRF/PIR GDE The multiple alignment editor can output an alignment in different formats: GCG/MSF, CLUSTAL, NBRF/PIR, and GDE. The multiple input and out put capacity of DNAMAN makes it compatible with major sequence analysis software.Phylogenetic treesDNAMAN calculates the ho

38、mology matrix and establishes related distances between all pairs of sequences. Consequently, DNAMAN can output a distance matrix of multiple alignment, and draw phylogenetic trees or homology trees. You can carry out bootstrapping tests for the confidence value of a phylogenetic tree.Restriction an

39、alysisIf the sequences in multiple alignment editor are DNA, you can perform a restriction analysis on these sequences. This analysis is useful in restriction site comparison of aligned DNA sequences.Hydrophobic / hydrophilic profilesIf the sequences in multiple alignment editor are protein, you can

40、 plot the hydrophobic or hydrophilic profile of all sequences for comparison.Protein secondary structure predictionDNAMAN predicts the secondary structure of multiple protein sequences using the DSC method developed by King and Sternberg.Primer AnalysisPrimer designMelting temperature predictionComp

41、lementarity of primersMispriming analysisSilent mutation primersDirected mismatch primersPrimer designThe function of primer design includes not only primer filtration by Tm, but also mispriming and restriction analyses on the primers. DNAMAN can help you to find optimal primers that satisfy your re

42、quirements.DNAMAN allows you to set numerous control criteria for optimal primer filtration, such as the regions of target DNA, size of PCR products, primer characteristics, reaction conditions and primer configurations.You can carry out a restriction analysis on the primers in order to select those

43、 with or without restriction site(s). You can discard the primers that are easy to anneal to secondary sites of target DNA using mispriming analysis.Melting temperature predictionDNAMAN calculates and reports the thermodynamic Tm, hybridization Tm, and GC+AT Tm of DNA-DNA hybridization. You can also

44、 have the Tm information on the hybridization of DNA-RNA and RNA-RNA. These Tms can be used for PCR primers as well as hybridization probes.Complementarity of primersPrimer complementarity may affect the performance of PCR primers or hybridization probes. DNAMAN analyzes the following three kinds of

45、 primer complementarity.Self-complementaryDNAMAN searches for the most possible self-complementary configuration of primers with the lowest free energy. Complementarity with target DNA DNAMAN searches for the complementary sequences between the primer and both stands of target DNA. Two primer comple

46、mentarity DNAMAN searches for complementary sequences between two primers. It reports the continuous and discontinuous complementary sequences.Mispriming analysisWith mispriming analysis you can search for all possible annealing sites of a primer on target DNA sequence. DNAMAN allows you to set up S

47、core matrix: perfect match, mismatch and G-T match; Position weight matrix, Gap penalty and Cut-off score. This analysis can eliminate PCR primers that are easy to anneal to secondary sites.Silent mutation primersSilent mutation analysis allows you to design a desired mutation site on a DNA sequence

48、. This mutation will result in the modification of restriction property without changing the coding amino acid sequence. This function searches for potential mutation positions to create or destroy restriction enzyme sites. You can use this function to design primers to create a silent muation on ta

49、rget DNA sequence.Directed mismatch primersDirected mismatch analysis allows you to create or remove restriction sites on a DNA sequence or its mutants (variants) by incorporating mismatch at a site near the mutation. Using this function you can design PCR primers to create or destroy a restriction

50、site in order to distinguish the wild type allele and a common mutant allele.TranslationandProteinAnalysisTranslationGeneticcodetableReadingframeoverviewCodonusageanalysisAminoacidcompositionProteinhydrophobicandhydrophilicprofileProteinchargeandpIanalysisProteinsecondarystructurepredictionReversetr

51、anslationTranslationDNAMAN deduces protein sequences from three reading frames of a DNA sequence and displays results with many options. By setting the number of amino acid per one line, you can change the layout of the translation file.DNAMAN allows you to select any region from a sequence file, an

52、d perform translation analysis. In the report file DNAMAN shows both translated and untranslated regions.Genetic code tableDNAMAN provides seven genetic code tables with the options of adding new code tables or editing any existing one. You may select any genetic code table for translation and prote

53、in analysis.Reading frame overviewDNAMAN presents a graphical overview on six reading frames of a DNA sequence. It is a useful feature to locate the ORFs on a large DNA sequence.Codon usage analysisDNAMAN provides a codon usage table for any reading frame of a DNA sequence. The table indicates the n

54、umber and frequency of each codon used in a reading frame.Amino acid compositionDNAMAN reports the amino acid composition, pI and molecular weight of a protein sequence.Protein hydrophobic and hydrophilic profileDNAMAN shows protein hydrophobic and hydrophilic profiles in a graphic window that may h

55、elp you to predict hydrophobic clusters or antigen regions in a protein sequence. The graphical profiles are editable to produce high quality illustrations for publications. Protein charge and pI analysisDNAMAN calculates protein charge at a given pH. It shows also the predicted isoelectric point of

56、 the protein. In addition, DNAMAN can deduce the suitable buffer pH for a desired charge.Protein secondary structure predictionDNAMAN predicts the secondary structure of a protein sequence using the DSC method developed by King and Sternberg.Reverse translationDNAMAN provides the reverse translation

57、 of a protein sequence. It reports the reverse translated DNA sequence with ambiguous nucleotides at variant positions. This feature can be used to degenerate primers from peptide sequences.DatabaseManagementOligodatabaseDNAandproteindatabaseSearchinginDNAorproteindatabaseOligo databaseYou may have

58、a large number of oligo nucleotides for experiments of sequencing, blotting, PCR, etc.DNAMAN provides an oligo database manager that can help you to effectively organize and use these oligoes.When you create oligo databases for different projects. DNAMAN allows you to attach a password for the security of the database.Any